chr22-19039043-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005137.3(DGCR2):c.1475G>A(p.Arg492His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00148 in 1,612,962 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R492C) has been classified as Uncertain significance.
Frequency
Consequence
NM_005137.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGCR2 | NM_005137.3 | c.1475G>A | p.Arg492His | missense_variant | 10/10 | ENST00000263196.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGCR2 | ENST00000263196.12 | c.1475G>A | p.Arg492His | missense_variant | 10/10 | 1 | NM_005137.3 | P1 | |
DGCR2 | ENST00000389262.8 | c.*1046G>A | 3_prime_UTR_variant, NMD_transcript_variant | 11/11 | 1 | ||||
DGCR2 | ENST00000537045.5 | c.1352G>A | p.Arg451His | missense_variant | 9/9 | 2 | |||
DGCR2 | ENST00000467659.1 | n.1253G>A | non_coding_transcript_exon_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00235 AC: 358AN: 152218Hom.: 4 Cov.: 34
GnomAD3 exomes AF: 0.00297 AC: 734AN: 247198Hom.: 8 AF XY: 0.00276 AC XY: 371AN XY: 134352
GnomAD4 exome AF: 0.00139 AC: 2033AN: 1460626Hom.: 28 Cov.: 30 AF XY: 0.00135 AC XY: 984AN XY: 726638
GnomAD4 genome ? AF: 0.00234 AC: 357AN: 152336Hom.: 4 Cov.: 34 AF XY: 0.00361 AC XY: 269AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | DGCR2: BP4, BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at